Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

Authors: CONGRAINS, CARLOS - University Of Hawaii; DUPUIS, JULIAN - University Of Kentucky; RODRIGUEZ, ERICK - Florida Department Of Agriculture; Norrbom, Allen; STECK, GARY - Florida Department Of Agriculture; SUTTON, BRUCE - Florida Department Of Agriculture; NOLAZCO, NORMA - National Service Of Agrarian Health; DE BRITO, REINALDO - Universidade Federal De Sao Carlos; Geib, Scott

Submitted to: Evolutionary Applications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/10/2023
Publication Date: 8/30/2023
Citation: Congrains, C., Dupuis, J., Rodriguez, E.J., Norrbom, A.L., Steck, G., Sutton, B., Nolazco, N., De Brito, R.A., Geib, S.M. 2023. Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex. Evolutionary Applications. 16(9):1598-1618. https://doi.org/10.1111/eva.13589.
DOI: https://doi.org/10.1111/eva.13589

Interpretive Summary: The South American fruit fly (Anastrepha fraterculus) is really a group of very closely related species forming a species complex called the "fraterculus group". Several members of this complex are some of the most economically important pest species in the new world, including South and Meso-america. Accurate discrimination of these species is difficult using morophological characters, and genetic tools are limited to accurately discrimiate across the complex. In this report, using whole genome sequencing, a series of fraterculus complex members were sequenced and novel markers were developed to generate a robust phylogentic analysis of the group. Thousands of markers across the genome were used to discriminate species in this genome wide analysis, but in a practical context, we defined as few as 80 mutations in the genome that could be sub-sampled in an applied diagnostic approach to likely discriminate species in this group. This report demonstrates the utility of genome-wide datasets for both accurately defining species boundaries and also as a resource to develop diagnostic tools from for accurate identification.

Technical Abstract: Insect pests cause tremendous impact to agriculture worldwide. Species identification is crucial for implementing appropriate measures of pest control but can be challenging in closely related species. True fruit flies of the genus Anastrepha Schiner includes some of the most serious agricultural pests in the Americas, with the Anastrepha fraterculus (Wiedemann) complex being one of the most important due to its extreme polyphagy and wide distribution across South America and Mesoamerica. Species from this complex and other closely related species are classified into the fraterculus species group, which is exemplified by unresolved evolutionary relationships due to incomplete lineage sorting and introgression. Here we performed multifaceted phylogenomic approaches using data from thousands of genes to unravel the evolutionary relationships of the A. fraterculus complex to provide the baseline for molecular diagnosis of these pests. We developed a workflow to accommodate variable sources of data (transcriptome, genome assembly, and whole-genome shotgun sequencing) to infer, align, and filter ortholog genes, and generate robust and reliable datasets for phylogenetic studies. From this dataset, we reconstructed thousands of gene trees that displayed high levels of discordance. Nevertheless, the inferred coalescent trees were consistent across phylogenetic methods and datasets, except for one lineage in the A. fraterculus complex. Furthermore, species network analysis confirmed the presence of introgression across A. fraterculus group lineages. Our findings generated a high-quality phylogeny of the group, providing insights to the intricate patterns of evolution of the A. fraterculus complex, and support the hypothesis that it is an assemblage of closely related cryptic lineages that have evolved under interspecific gene flow. Notably, despite this complex divergence scenario, our subsampling analysis revealed that a set of as few as 80 loci has similar phylogenetic resolution as the genome scale dataset, offering a foundation to develop better diagnostic tools in this species group.